ArticleNucleic acids research2021
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Comparative Transcriptomic Analysis Reveals Conserved and Nutrient-Specific Responses to Nutrient Deficiencies in Quinoa.Plants (Basel, Switzerland) · 2026Article
- Whole-genome analysis of Brevibacterium sanguinis AZMABM HM27: a bacterial isolate from the sea anemone Radianthus magnifica and exhibiting promising multi-therapeutic properties.Molecular biology reports · 2026Article
- Genetic and functional characterization of loss of growth superiority of 22-ploid Morus nigra L. (2n = 22x = 308).Molecular biology reports · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae).G3 (Bethesda, Md.) · 2026Article
- Whole genome sequence data of thermotolerantData in brief · 2026Article
- Transcriptomic dataset of the invasive speciesData in brief · 2026Article
- Genome assemblies of the liverwort Blasia pusilla uncover a well-defined pseudoautosomal region on homomorphic UV sex chromosomes.Genome biology · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Transcriptomic Regulation of Aquaporins During Seed Germination in the Marine SeagrassPlants (Basel, Switzerland) · 2026Article
- Macroevolutionary changes in gene expression response to an immune stimulus across the diversity of fishes.Molecular biology and evolution · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Phosphoproteomic identification of Mos-MAPK targets in meiotic cell cycle and asymmetric oocyte divisions.The Journal of cell biology · 2025Article
- The structure and allelic diversity of the self-incompatibility locus (S-locus) in diploid potatoes inferred from genome sequences and transcriptome data from styles and pollen.The plant genome · 2025Article
- Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.Nature communications · 2025Article
- Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts.Microbial ecology · 2025Article
- A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.The plant genome · 2025Article
- De novo transcriptome assembly and discovery of drought-responsive genes in white spruce (Picea glauca).PloS one · 2025Article
- From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.BMC genomics · 2024Article
- Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation.Nature communications · 2024Article
- Multi-omic analysis tools for microbial metabolites prediction.Briefings in bioinformatics · 2024Review
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID's unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
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